Submitting full clinical tests in bulk using Excel

This document provides detailed information about how to submit data to the GTR describing the clinical tests you offer, via files you prepare in advance. Templates for the files to be uploaded are available from GTR's ftp site and from your laboratory's overview page. Bulk submission of research tests is not enabled. For information on the other submission scenarios and formats available, please see http://www.ncbi.nlm.nih.gov/gtr/docs/submit/#scenarios.

General Requirements

All submission scenarios require that you first register your laboratory in the GTR using the interactive submission website.

  • Establish a login in MyNCBI
  • You can register a new laboratory
  • If your laboratory has already been registered by another laboratory staff member, please contact GTR staff to have your MyNCBI login connected to the laboratory group account.

Prepare a submission using only the GTR full test submission template.

  • Familiarize yourself with this submission scenario by reviewing the detailed instructions.
  • Download a full test submission template file from the GTR ftp site, or download your lab-specific full test submission template on your lab overview page.
  • To access your lab-specific spreadsheet templates, log into the GTR submission site at https://submit.ncbi.nlm.nih.gov/subs/gtr
  • Click on your laboratory name, or the 'Review lab submission' button, both found at the top of your GTR submission homepage.
  • Scroll down the page to the 'Tests' section. There you will see the following template types and download options:
    • Download blank minimal clinical test fields spreadsheet
    • Download blank spreadsheet with all clinical test fields
    • Request to download previously submitted data on a spreadsheet with all clinical test fields (Link will be emailed to you for download)
  • Complete the file according to instructions.
  • Use the 'Upload your bulk submission file' button at the bottom of the overview tab of your lab record to upload your completed file.
  • Correct any processing errors, if found. The entire spreadsheet must pass validation; specific error-free tests will not be processed separately.
  • Review the submitted test records on the GTR public web site 24-48 hours after successfully uploading the spreadsheet. Data can be edited using the GTR submission user interface or the full test submission template (see how to edit a test using the full test submission template).
  • Instructions for completing the full test submission file
    • Adding a new test
    • Editing an existing test
    • Deleting an existing test
  • Definitions and column values
  • Possible error messages
  • Steps to upload a completed file
  • enter one test first,
  • use the copy function in your worksheet software to create more rows, and then
  • edit only the cells in each row that define what is different about each test, such as the order code, test methodologies, etc.
  • Note: Supporting documents, such as FDA approval documents and sample reports cannot be uploaded via the full test submission template. If you wish to add these files, please do so manually within the GTR submission interface found at https://submit.ncbi.nlm.nih.gov/subs/gtr.

Detailed instructions about completing the test submission file and submitting it

Instructions for completing the full test submission file

General features of the test submission file

This spreadsheet is used to provide the full set of test-specific data for clinical tests to GTR.  The template includes minimal, recommended and optional fields. Registration of each test is complete after the spreadsheet is successfully uploaded. You can add or edit fields at a later time using either the full test submission template, or by using the GTR submission user interface. For definitions of minimal, recommended, and optional fields, please go here.

The file does not have to reflect all tests offered by your laboratory.  You can prepare and submit multiple test submission files. You can also enter and/or edit tests by using the interactive submission site.

Please do not edit rows that start with a # or that have a colored background.

A red triangle in the upper right of a cell indicates there is a comment. Hover over these cells to see abbreviated instructions on how to complete that cell.

Columns C, J, M, N, O, Q, R, U, X, AD, AE, AF, AG, AH, AL, AO, AT, AV, AX, AY, BA, BC, BO, BS, BU, BV, BY, CE, CG, CJ, CK, CM, CS, CT, CU provide pull-down menus.  To complete those fields,  first click the cell.  A gray arrow will appear to the right of the cell. Click on the arrow to see the menu of allowed values and select from it. If you need to select multiple values click on the cell below to add another value.  Please note carefully how to manage definitions of a test using multiple rows in the spreadsheet.

If order codes are unique for each test in your lab, and your lab does not have an internal tracking identifier, you can use the order code as your Test tracking ID.

The first column and the first row are frozen as default. However, you may want to unfreeze the first column or freeze another column (e.g. order code) to help keep track of which test you are working on. To do this go to the 'View' tab of the spreadsheet and click the freeze panes icon.

How to enter data

The form contains all available columns, or data fields, which you can use to provide data for a test. The first column is critical, because if your submission requires more than one row to describe a test completely, the value in the first column is used to recognize that these data all belong to the same test. In general, each row corresponds to a test target description. A test target is what the test interrogates (e. g. the analyte, chromosomal region/mitochondrion, gene or protein). For simple tests (i.e. one test target), one row corresponds to one test you want to register in GTR. Each set of test targets and linked attributes (e.g. condition the target is assessing, target category, name of what is tested, variants, RefSeq:exons) must be entered in one row so GTR can identify their interrelationship. Thus, a test with multiple test targets will have multiple rows, each with the same value in column A.

Each set of rows with the same Test tracking ID is processed as one test. For single tests that are described using multiple rows, please enter the same Test tracking ID in column A for each applicable row. GTR identifies specific tests via the Test tracking ID, therefore it is crucial that each test be assigned a unique id of your choosing.

The action column designates whether you are adding a new test, or editing or deleting an existing registered GTR test. If you are editing or deleting an existing GTR test, you MUST include the GTR test accession in column B. You can find the test accession number in your list of tests on the GTR submission site (far right column).

Each test target must be linked to at least one indication (condition or phenotype name). Multiple indications for the same test target can be separated by |. Indications placed in the same row as a test target will be connected to that specific target.

If the same indication (condition or phenotype) relates to more than one test target it must be repeated for each appropriate test target row.

Indications (condition or phenotypes) may be entered either as names or MIM numbers. We recommend that you search GTR to find condition/phenotype names recognized by GTR. Use of a recognized condition/phenotype name facilitates discovery of your test through the autocomplete dictionary and disease hierarchies, and enables your test to be linked to clinical, literature and consumer resources.

GTR does not accept registration of send-out tests (i.e. tests that are performed entirely at an outside laboratory/facility as explained here). At least one test component must be performed at the laboratory that is registering the test. If any part of the test is performed at an outside facility, you may enter No for 'Test performance location' on the spreadsheet. In the next column, you should specify which components of the test are performed at an outside facility and subsequently provide additional information in the following comment cell.

For column/fields that have menu choices, you must select from the choices provided. If multiple choices are applicable, each must be entered in the row(s) below.

Sample tests

A file with sample tests in the full test submission template can be downloaded here.

The sample tests are as follows:

Test 10001 demonstrates completion of all fields except for those recommended or optional fields which are not applicable

Test 10002 demonstrates completion of minimal fields only

Test 10003 demonstrates completion of minimal and applicable recommended fields

Definitions and column values

This table describes each value in the columns of the test submission file. The status column below (see key) indicates whether the field must be supplied to enable successful upload of the file and the impact on public display. On the full test submission template, minimal fields are highlighted so that they are differentiated from recommended and optional fields.

Four columns are applicable only to the spreadsheet: (A) *Test tracking ID, (B) GTR accession, (C) Action * and (BR) Condition/phenotype: choose name or MIM number. All of the remaining columns correspond to fields that are part of overall GTR test submission.

Key for Status column:

Private = field will not display to the public

Public = field will be viewable by GTR users

Minimal = field must be completed for this file to be processed successfully

Recommended = field will display as 'Not provided' if left blank

Optional = field will not display to the public if left blank (i.e. if not applicable for the test)

Lab Test Tab

Column Status Description Hints
A

Minimal

Private

Test tracking ID ID to distinguish one test from another on this spreadsheet. This field must be completed for each line. If a single test has multiple lines of data, this field must have the same value for all lines of that test. If you have an internal ID, which will help you track your submission, provide it here. You can use your order code if unique for each test or you can come up with your own unique tracking code (e.g. 1,2,3,4,...)
B

Minimal* (if updating or deleting)

Private

GTR Accession Test ID to identify the GTR test you wish to edit or delete. This field should be empty if you are adding a new test, and must be completed if you are updating or deleting a test previously registered in the GTR.
C

Minimal

Private

Action

Field used to determine which action to perform on the row(s) corresponding to a single test. Only enter once per test. Selections include:

  • Update: Edit an existing GTR test
  • Delete: Permanently remove an existing GTR test
  • Add New: Create a new test registration
  • No Change: Do nothing to the existing test registration
D

Recommended

Public

Test order code Enter the test order code, commonly found on the laboratory's requisition form, test menu or test catalog. This is the code health care providers (for example) would use to order the test through the laboratory. Complete this field only for the first line of data for each test.
E

Minimal

Public

Laboratory test name Test name as found on the lab test menu or requisition form. By default, test name is the record name in GTR and this is how you can easily identify your tests in your submission homepage. Complete this field only for the first line of data for each test.
F

Optional

Public

Laboratory test short name The short test name is the shortened name or mneumonic used by the lab to identify the test. This may be a test name used in conjunction with a test order code for quick test menus, electronic medical records or HL7 systems and programs. Examples include: CHD7Full. Complete this field only for the first line of data for each test.
G

Optional

Public

Manufacturer's test name Enter the manufacturer's name of the commerical test or kit used if in the submitted assay. If the test is an entirely laboratory developed test, there should not be a manufacturer's test name. Complete this field only for the first line of data for each test.
H

Optional

Public

URL for the test Enter the URL for test-specific information on your laboratory's website. URLs should be entered with the appropriate prefix, i.e., http:// or https://. Complete this field only for the first line of data for each test.
I

Optional

Private

Search terms Enter any search terms you wish to be associated with your submitted test. You do not need to enter keywords such as the disease/condition, gene, variant or test name. These will all automatically be included in a search. Relevant terms may include keywords such as archived or previously used test names. Limit to one search term per cell. Multiple search terms should be entered on multiple lines.
J

Minimal 

Public

Purpose of the test

Select the appropriate purpose or indication of the test. If you need to add multiple test purposes, use a new line for each purpose added. Definitions of choices can be found here. In the spreadsheet, you can select from the following list:

Diagnosis
Drug response
Monitoring
Mutation confirmation
Pre-implantation genetic diagnosis
Pre-symptomatic
Predictive
Prognostic
Recurrence
Risk assessment
Screening
Therapeutic management
K

Recommended

Public

Target population for this test Provide information on which population segment(s) the test is appropriate for and why. Complete this field once for each test. Example: Individuals with clinical symptoms consistent with Noonan syndrome.
L

Recommended

Public

Citations for target population PubMed identifiers preferred; otherwise, full citations or URLs. If multiple, separate by '|'. This will allow GTR to provide a link for users to have easy access to the citation. You can also provide a link to your lab's webpage with information about the target population for this test.
M

Optional

Public

Has there been FDA review of this test? Select the option (Y/N) corresponding to if the test or any portion of the test including reagents has been reviewed or is pending review by the FDA. This field should only be completed once per test.
N

Optional

Public

If no FDA review, FDA category designation

Select the appropriate option from the available choices:

FDA exercises enforcement discretion
Not applicable

O

Optional

Public

If FDA review, item reviewed This field is completed only when 'yes' is selected from the 'Has there been FDA review of this test?'. From the options indicated, select the portion of the test that has been reviewed or is pending review by the FDA. If multiple items reviewed, enter each item on a new line. Choices include:

ASR - Analyte-specific reagents
Assay(s)
IVDMIA - In Vitro Diagnostic Multivariate Assay(s)
Instrument(s)
Test kit(s)
Other- Please specify

P

Minimal* (if 'Other' selected in item reviewed)

Public

Item reviewed, 'Other' value Enter the text corresponding to the 'Other' value for Item reviewed.
Q

Optional

Public

If FDA review, FDA category designation This field is completed only when 'yes' is selected from the 'Has there been FDA review of this test?'. From the options indicated, select the category of FDA review. Choices include:

FDA exercises enforcement discretion
IUO - Investigational Use Only -The performance characteristics of this product have not been established.
IVD - In Vitro Device
RUO - Research Use Only- Not for use in diagnostic procedures.
Not applicable

R

Optional

Public

If FDA review, FDA regulatory status This field is completed only when 'yes' is selected from the 'Has there been FDA review of this test?'. From the options provided, select the status of the item reviewed. Choices include:

FDA cleared/approved
FDA exempt
Pending
Not submitted
Other-Please specify

S

Minimal* (if 'Other' selected in regulatory status)

Public

Regulatory status, 'Other' value Enter the corresponding 'Other' value for regulatory status.
T

Optional

Public

If FDA review, application number This field is completed only when 'yes' is selected from the 'Has there been FDA review of this test?'. Enter the FDA application number associated with the item reviewed.
U

Optional

Public

NYS CLEP status This field is required if 'NYS CLEP' is a valid certification for the specific test. Enter the status of the NYS CLEP approval for the test. This field should only be completed once per test. Options include:

Approved
Not approved
Pending
Grandfathered
Exempt

V

Minimal* (if licensed by NYS)

Public

NYS CLEP license number This field is required if 'NYS CLEP' is a valid certification for the specific test. Enter the license number provided by NYS CLEP for the approved test. This field should only be completed once per test.
W

Minimal* (if licensed by NYS)

Public

NYS CLEP expiration date This field is required if 'NYS CLEP' is a valid certification for the specific test. Enter the expiration date provided by NYS CLEP for the approved test. This should be a future date. This field should only be completed once per test.
X

Recommended

Public

Test development Select a single option for how the test was developed. Intended to help delineate the differences in certification requirements between the test types. Do not include reflex tests here. Options include:

FDA-reviewed (has FDA test name) -The test, test kit or reagents either have FDA approval or are currently in FDA review.
Manufactured (research use only; not FDA-reviewed) -The test or primary parts of the test are purchased from a commercial entity and have not gone through FDA review.
Modified FDA (has FDA-reviewed entry, but with lab modifications/field changes) -The test, test kit or reagents used in the test have undergone FDA review and are approved, however the submitting laboratory has augmented some part of the test or testing protocol.
Test developed by laboratory (no manufacturer test name) -This test is developed, produced and performed by the submitting laboratory. Also known as LDT.

Y

Recommended

Public

How to order (text description) Enter a description of the test ordering procedure, such as required forms, specimen handling/shipping instructions, etc. Requirements and recommendations about informed consent and genetic counseling can be discussed here. If applicable, a statement similar to the following can be used: “The laboratory recommends that pre- and post-test genetic counseling be offered and informed consent be obtained for this test but does not require documentation to accept and process the sample.” Complete this field only for the first line of data for this test.
Z

Recommended

Public

How to order (URL) Enter the URL for information on how to order the test. URLs should be entered with the appropriate prefix,i.e., http:// or https://. Complete this field only for the first line of data for this test.
AA

Recommended

Public

Test codes (URL) Enter the URL for information on corresponding codes related to the test, including CPT, ICD-9, ICD-10 and HCPCS codes. URLs should be entered with the appropriate prefix,i.e., http:// or https://. Complete this field only for the first line of data for this test.
AB

Optional

Public

LOINC codes The LOINC (Logical Observation Identifiers Names and Codes) database provides a set of universal names and ID codes for identifying laboratory and clinical test results. Enter the LOINC code. If applicable, the LOINC code can be found by using the 'Search' link, which will take you to the official LOINC website. The LOINC code must be entered manually, even if the submitter searches for the code using the link provided. Multiple codes should be entered on the same line, separated by '|'.
AC

Optional

Public

CPT codes Enter a molecular pathology CPT code. Enter one CPT code per line. If you do not know which code(s) are appropriate for your test, you can review code descriptors on the GTR submission site by clicking edit on your test (once submitted) and navigating to the 'How to Order' tab. You will have to review and accept the AMA CPT code agreement before accessing the code descriptors.
AD

Optional

Public

Who can order this test? Identify who can order the test based on the laboratory's policy on how the test can be ordered. Multiple selections should be made on multiple lines for the test.

Choose from the following options:

Genetic counselor
Health care provider
In-state patients
Licensed dentist
Licensed physician
Nurse practitioner
Out-of-state patients
Physician assistant
Public health mandate
Registered nurse

AE

Recommended

Public

Informed consent required?

Identify if the laboratory requires informed consent prior to performing the test. Select from the following choices:

Decline to answer
Required
Not required
As required by state law

If not required but recommended, you can comment in the 'How to order' text field.

AF

Recommended

Public

Pre-test genetic counseling required?

Identifiy if the laboratory requires genetic counseling prior to performing the test. Select from the following choices:

Decline to answer
Required
Not required

If not required but recommended, you can comment in the 'How to order' text field.

AG

Recommended

Public

Post-test genetic counseling required?

Identify if the laboratory requires genetic counseling after performing the test in order to release test results. Select from the following choices:

Decline to answer
Required
Not required

If not required but recommended, you can comment in the 'How to order' text field.

AH

Optional

Public

Test service

If applicable, select the laboratory services that are offered in conjunction with the specific test. Multiple selections are allowed, but enter each on a separate line. Please select each test service only once (you can provide multiple order codes for one service in the order code field). This field is different from 'Laboratory services' which allows submitters to select general services the laboratory provides. Choose from the following options:

Clinical testing/Confirmation of Mutations Identified Previously
Confirmation of Research Findings
Custom Balanced Chromosome Rearrangement Studies
Custom Deletion/Duplication Testing
Custom Sequence Analysis
Data Storage and Backup
Genetic Counseling
Identity Testing
Marker Chromosome Identification
Preimplantation Genetic Diagnosis (PGD)
Result Interpretation
Specimen Source Identification
Uniparental Disomy (UPD) Testing
X-Chromosome Inactivation Studies

For the complete, current list of choices for this field, see ftp://ftp.ncbi.nlm.nih.gov/pub/GTR/standard_terms/Test_services.txt.

AI

Minimal* (if 'Other' is selected in test service)

Public

Test service, 'Other' value Enter the corresponding 'Other' value for test-specific services.
AJ

Optional

Public

Test service order code If applicable, enter the order code for the test-specific service, commonly found on the laboratory's requisition form, test menu or test catalog. This is the code health care providers (for example) would use to order the service through the laboratory. If multiple services are entered, enter the associated order codes on separate corresponding lines.
AK

Optional

Public

Test service comment Enter further information to assist health care providers in ordering the test-specific services. An example includes, 'Pre-test and post-test genetic counseling is available for this test'. If multiple services are entered, enter the associated test-specific comment on separate corresponding lines.
AL

Optional

Public

Test additional service

If applicable, select the additional laboratory services that are offered in conjunction with the specific test. Enter multiple selections on separate lines. Please select each test service only once (you can provide multiple order codes for one service in the order code field). This field is different from 'Laboratory additional services' which allows submitters to select general services the laboratory provides. Options include:

Custom prenatal testing
Custom mutation-specific/Carrier testing

AM

Optional

Public

Test additional service order code If applicable, enter the order code for the test-specific additional service, commonly found on the laboratory's requisition form, test menu or test catalog. This is the code health care providers (for example) would use to order the service through the laboratory. If multiple services are entered, enter the associated order codes on separate corresponding lines.
AN

Optional

Public

Test additional service comment Enter further information to assist health care providers in ordering the additional test-specific services. An example includes, 'Once a mutation is identified, prenatal testing is available'. If multiple services are entered, enter the associated test-specific additional comment on separate corresponding lines.
AO

Recommended

Public

Specimen source

Select the specimen type(s) allowed for the test. Multiple selections allowed. Each specimen type should be on a separate line. Choices include:

Amniocytes
Amniotic fluid
Bone marrow
Buccal swab
Cell culture
Chorionic villi
Cord blood
Cystic hygroma fluid
...
Other: please specify

For the complete, current list of choices for this field, see ftp://ftp.ncbi.nlm.nih.gov/pub/GTR/standard_terms/Specimen_sources.txt.

AP

Minimal* (if 'Other' is selected for specimen source)

Public

Specimen source, 'Other' value Enter the corresponding 'Other' value for specimen source.
AQ

Recommended

Public

Specimen source URL Enter the URL to the laboratory's website that describes the specimen requirements and handling for the test. URLs should be entered with the appropriate prefix,i.e., http:// or https://.
AR

Recommended

Public

Testing strategy Describe the suggested sequence of ordering tests, discuss reflex testing, testing algorithms and related issues. This field is for recommendations on how to order the test in sequence of relevance to the patient (target population) being tested. This field should not include discussion of methodologies or test procedural  protocols. If describing reflex tests, each test component should be delineated. If a test is ordered, additional tests may be performed as necessary under certain circumstances based on initial results and that should be described in this field.
AS

Recommended

Public

Citations to support testing strategy Enter references and/or URLs as appropriate to further describe the testing strategy/algorithm.  If entering an URL, please specify the appropriate prefix, http:// or https://. PubMed identifiers preferred; otherwise, full citations or URLs. If multiple, separate by'|'.
AT

Recommended

Public

Test-specific contact policy

Select the policy of the laboratory regarding who (patients or health care providers) and when (pre-test/post-test/anytime) can contact the lab for this test. If appropriate, select multiple options with each option on a separate line. Options include:

Laboratory can only accept contact from health care providers. Patients/families are encouraged to discuss genetic testing options with their health care provider.
Post-test email/phone consultation regarding genetic test results and interpretation is provided to patients/families.
Pre-test email/phone consultation regarding genetic test results and interpretation is provided to patients/families.

AU

Recommended

Public

Test-specific contact person

From the drop-down list, select the test-specific contact for thes test. This individual's name and contact information will be displayed on the test page for health care providers to view. If no test-specific contact is provided, the laboratory's general contact information will display. For multiple contacts, add each person on a separate line.

Note: If you do not see the staff member's name you want to select in the personnel list, you either have downloaded a generic full test submission template (and not a pre-loaded laboratory-specific template) or, you need to add the person to your laboratory registration. Either way, you will not be able to add the person on the spreadsheet you are currently working on. We recommend skipping this field on your current spreadsheet and then manually adding the test-specific contact using the GTR submission site. See http://www.ncbi.nlm.nih.gov/gtr/docs/submit/test_order/for more information.

AV

Minimal

Public

Test performance location(s):

Select where the test is performed from the following options. Tests which are performed entirely at an outside lab/facility should not be registered in GTR. 'In-house' means within the lab/facility covered by the same CLIA certification number. 'Outside lab' means a different lab/facility than that dovered by your CLIA certification, even if both labs have the same parent organization. Multiple selections are allowed,unless the entire test is performed in-house. Select each option on a separate line.

Entire test performed in-house
Interpretation performed at an outside lab

Interpretation performed both in-house and at an outside lab
Interpretation performed in-house
Report generated at an outside lab
Report generated both in-house and at an outside lab
Report generated in-house
Specimen preparation performed at an outside lab
Specimen preparation performed both in-house and at an outside lab
Specimen preparation performed in-house
Wet lab work performed at an outside lab
Wet lab work performed both in-house and at an outside lab
Wet lab work performed in-house

AW

Minimal* (if any part of the test is peformed outside the registering laboratory)

Public

Test performance location(s) comments Briefly describe methods and location for components of test work done at an outside lab.
AX

Minimal

Public

Method Category

Category of the method(s) being used in this test. If multiple methods are used in the test, add an additional line for each method. If your test uses more than one Test method per Method Category, you must select the category again in column AX to correspond to the value in column AY. To display the complete list of choices, please:

1. Click on the cell - an arrow displays to the right of the cell, then
2. Click on the gray arrow.

Options include:

Analyte
Multicolor FISH (M-FISH)/Spectral Karyotyping
Chromosome breakage studies
Deletion/duplication analysis
Enzyme assay
FISH-interphase
FISH-metaphase
...
For the complete, current list of choices for this field, see ftp://ftp.ncbi.nlm.nih.gov/pub/GTR/standard_terms/Method_category.txt.
AY

Minimal

Public

Test method

Select the test method that corresponds to the entry selected in column 'AX' for Method category. Each test must have an entry both in column 'AX' and column 'AY'. If the test has multiple test methods, add each test method on a new line, making certain the Test method value corresponds to the value in Method category. If the test method used in this test is not listed, please select 'Other' from the list in the spreadsheet and specify the test method in column 'AZ'.

To display the complete list of choices, please:

1. Click on the cell - an arrow displays to the right of the cell, then
2. Click on the gray arrow.

Options include:

Allele-specific primer extension (ASPE)
Alternative splicing detection
Bi-directional Sanger Sequence Analysis
C-banding
Chromatin Immunoprecipitation on ChIP
Comparative Genomic Hybridization
...
For the complete, current list of choices for this field, see ftp://ftp.ncbi.nlm.nih.gov/pub/GTR/standard_terms/Primary_test_methodology.txt.
AZ

Minimal* (if 'Other' is selected for test method)

Public

Test method, 'Other' value Enter the corresponding 'Other' value for test method.
BA

Recommended

Public

Instruments used for test method

Name the instrucment used for a specific methodology. Enter each instrument on a separate line, corresponding to the appropriate test method.

Affymetrix GeneChip Scanner 3000 7G Whole-Genome Association System
Affymetrix GeneTitan® MC
Affymetrix HotStart-IT Probe qPCR Master Mix with UDG (2X)
Agilent 2100 Bioanalyzer
Agilent SureSelect
...

For the complete, current list of choices for this field, see ftp://ftp.ncbi.nlm.nih.gov/pub/GTR/standard_terms/Instruments.txt.

BB

Minimal* (if 'Other' is selected for instruments)

Public

Instruments, 'Other' value Enter the corresponding 'Other' value for instruments.
BC

Optional

Public

Platforms

Select the name of a platform used in your test, if appropriate. If you use a platform not on the list, choose 'Other' and then provide the name.  A platform name typically corresponds to a unique catalogue number or a set of catalogue numbers which are bundled with other consumables. The format is usually manufacturer name, product name, and general specifications.

Affymetrix CytoScan HD Array
Affymetrix Gene Profiling Array cGMP U133 P2
Affymetrix GeneChip Human Genome U133 Plus 2.0 Array
Affymetrix GeneChip Human Mitochondrial Resequencing Array 2.0
Affymetrix Genome-Wide Human SNP Array 6.0
...

For the complete, current list of choices for this field, see ftp://ftp.ncbi.nlm.nih.gov/pub/GTR/standard_terms/Platforms.txt.

BD

Minimal* (if 'Other' is selected for platform)

Public

Platform, 'Other' value Enter the corresponding 'Other' value for platforms.
BE

Optional

Public

Test procedure or protocol Summarize the methodology and descrie the specific steps for each method of the assay.
BF

Optional

Public

Citations to support test procedure or protocol Provide citations or URL for the protocol. PubMed identifiers preferred; otherwise, full citations or URLs. If multiple, separate by'|'. URLs should be entered with the appropriate prefix,i.e.,http:// or https://.
BG

Recommended

Public

Confirmation of test results Describe whether and how test results are confirmed (beyond initial validation of the assay). For example, 'Positive results are confirmed on a new DNA preparation using sequence analysis'.
BH

Optional

Public

Test comment Provide textual description of the test methods or any other information about your test not described elsewhere that may be useful to clinicians ordering your test, e.g. 'Bi-directional sequencing of exons 1-5 with concurrent analysis of NP_000000.0:p.Glu234Gly'.
BI

Minimal

Public

Analytical Validity

The Analytical validity field needs a statement that includes quantitative information for analytical sensitivity, analytical specificity, accuracy, and/or precision of this test. General statements about methodologies that do not contain specific information about the test do not satisfy the specifications for this field. Nor do statements such as "N/A", "not applicable", "Yes" or "unknown". Example: 'The OtoChip is greater than 99% sensitive for detecting substitution variants in the sequence analyzed. In addition, this assay is 95% sensitive for detecting small insertions or deletions (inDels), and 100% for 1-2bp indels, 92.3% for 3-5bp indels and 87.5% for >10bp indels.'

BJ

Recommended

Public

Citations to support analytical validity Provide PubMed ID when available, otherwise full citations or URLs. If multiple, separate by'|'.  URLs should be entered with the appropriate prefix, i.e., http:// or https://. This will allow GTR to provide a link for users to have easy access to the citation. If no publications are available, provide non-proprietary internal lab data in analytical validity statement, if available. You can also provide a link to your lab's webpage with information about analytical validity for this test.
BK

Recommended

Public

Clinical validity Clinical validity is how consistently and accurately the test detects or predicts the intermediate or final outcomes of interest. This information will display in the Overview and Indication tabs of the test record. Describe clinical sensitivity and specificity, positive and negative predictive values, the population(s) assessed, adn the number of specimens used to calculate clinical validity. Clinical sensitivity is the proportion of positive test results among patients with the defined clinical presentation. Clincal specificity is the proportion of negative test results among patients witout the defined clinical presentation.  Positive predictive value is the chance of having the marker among those that test positive. Negative predictive value is the chance of not having the marker among those that test negative.
BL

Recommended

Public

Citations to support clinical validity Provide citations to support clinical validity statment. Provide PubMed ID when available, otherwise full citations or URLs. If multiple, separate by '|'. URLs should be entered with the appropriate prefix, i.e., http:// or https://.
BM

Recommended

Public

Assay limitations Describe any factors that affect the value of the test for its intended use. Includes limits of detection and validation of test for only specific subpopulations or particular uses.
BN

Recommended

Public

Citations to support assay limitations Provide citations to support assay limitation statements. Provide PubMed ID when available, otherwise full citations or URLs. URLs should be entered with the appropriate prefix, i.e., http:// or https://. If multiple, separate by '|'.
BO

Recommended

Public

Clinical utility category

Select a category from the list and support it with an URL and/or citations. Enter multiple clinical utitity statements on separate lines. Choose from the following options:

Avoidance of invasive testing
Establish or confirm diagnosis
Guidance for management
Guidance for selecting a drug therapy and/or dose
Lifestyle planning
Predictive risk information for patient and/or family members
Reproductive decision-making
Sufficient research has not been conducted to establish utility of the test
Other (please specify)

For the complete, current list of choices for this field, see ftp://ftp.ncbi.nlm.nih.gov/pub/GTR/standard_terms/Clinical_utility_categories.txt.

BP

Minimal* (if 'Other' is selected for Clinical utility category)

Public

Clinical utility category other value Enter the corresponding 'Other' value for Clinical utility category.
BQ

Minimal* (if a clinical utility category is chosen, a citation or URL is required)

Public

URL to explain clinical utility Cite recommendations or practice guidelines for the test that have been issued by authoritative groups. Some practice guidelines may be available via URL but not a citation. URL to the laboratory web page may be used. URLs should be entered with the appropriate prefix, i.e., http:// or https://.If multiple clinical utility statements, enter on separate lines, with each corresponding to the appropriate entry in column BO.
BR

Minimal* (if a clinical utility category is chosen, a citation or URL is required)

Public

Citations to support clinical utility Provide citations to support clinical utility statements. Provide PubMed ID when available, otherwise full ciations. URLs should be entered with the appropriate prefix, i.e., http:// or https://. If multiple clinical utility statements, enter on separate lines, with each corresponding to the appropriate entry in column BO. If multiple citations for a single clinical utility statement, enter on the same row, but separate by '|'.
BS

Minimal

Private

Condition/phenotype: choose name or MIM number

Select whether the condtion/phenotype will be provided by GTR preferred name or MIM number. You can find the GTR preferred name by searching the public web site at http://www.ncbi.nlm.nih.gov/gtr. In the spreadsheet, you can select from the following list:

MIM number
Condition name

BT

Minimal

Public

Conditions/Phenotypes

If you selected MIM number in previous column (BR), enter the valid MIM condition number (please do not enter MIM number for gene records). If you enter a MIM number for the condition being tested, GTR will use this to match your submission to disorders already represented in GTR's database.

The list of names GTR uses per MIM number is provided from the ClinVar's FTP site.

If you selected condition name in column BR, write the preferred name of the condition/phenotype. You can search the GTRto find the condition name in the database. Linking to an existing condition name ensures that this test will be connected to available resources such as clinical and molecular resources. Learn how to use MedGen to select condition and phenotype terms.

If multiple conditions/phenotypes exist for a single target (columns BT through BV), enter values separated by a vertical bar (|). If same condition/phenotype exists for multiple targets, the conditon/phenotype must be repeated on each target line.

BU

Minimal

Public

Germline or Somatic

Select the type of target from the following options:

Germline
Somatic
Both

BV

Minimal

Public

Target category

 

Select the category describing the test target measures in the test. If multiple targets are being tested, add each target on a separate line. In the spreadsheet, you can select from the following list:

analyte
chromosomal region/mitochondrion
gene
protein

Note thatgeneis used to represent molecular assays that detect variations in a gene or set of genes.

BW

Minimal

Public

Name of what is tested

If gene in column N, enter HGNC official gene symbol. If chromosomal region/mitochondrion in N, enter region. If protein, please use Swiss-Prot protein name. If an analyte, enter its name. If multiple targets are being tested, each target must be stored on a separate line.

Examples:

Analyte: 'Branched-chain amino acids' or the enzyme 'Branched-chain ketoacid dehydrogenase'

Chromosomal region/mitochondrion: '11q15' or 'm.7446-m.7514'

Gene: 'CDKN2A' or 'CFTR'

Protein: 'Hemoglobin subunit beta' or 'Adenomatous polyposis coli protein'

BX

Optional

Public

Variants(s)

Describe variation using fully qualified HGVS expression,e.g.NM_000258.2:c.427G>A. If multiple variants for Conditions/phenotypes named in M, separate with '|'. Fill this column only if gene is provided in columns N.

Example: for a test that interrogates the 1477_1478delCA and 1477C>T of the CFTR gene for Cystic fibrosis, you would enter:

Column BR: MIM number
Column BS: 219700
Column BT: Germline
Column BU: gene
Column BV: CFTR
Column BW: NM_000492.3:c.1477_1478delCA|NM_000492.3:c.1477C>T
BY

Optional

Public

Clinical significance of variant

Assign the clinical significance of the variant(s) entered in column BW. Options include:

Association
Confers sensitivity
Drug response
No known pathogenicity
Not provided
Other
Pathogenic
Probably not pathogenic
Probably pathogenic
Risk factor
Variant of unknown significance

For the complete, current list of choices for this field, see ftp://ftp.ncbi.nlm.nih.gov/pub/GTR/standard_terms/Clinical_significance.txt.

BZ

Optional

Public

Citations to support the clinical significance

Provide citations to support assay limitation statements. Provide PubMed ID when available, otherwise full citations or URLs. URLs should be entered with the appropriate prefix, i.e., http:// or https://. If multiple, separate by '|'. Citations should be entered on lines corresponding to associated clinical significance statment, entered in column BX.

CA

Optional

Public

RefSeq:relevant exons

Provide details about the exons analyzed and specify the associated reference sequences. Format by first specifying reference sequence, include assession number and version, then using ':', and then listing exons. If multiple reference sequences per gene, separate these by '|'.

Valid only if gene is provided in column N. The RefSeq defining the exon numbering system must be supplied in this column.

Example: NM_4433221.1:1-5(all)|NM_123456.1:1,3,4-5 including 5 bp in intron-exon boundaries.

If a continuous range is tested: provide the exon numbers as a range,e.g. 2-5. If the range includes all exons, add (All),e.g. 1-5 (All)

If a subset is tested: enumerate the exons tested. Ranges are allowed,e.g.3,5,9-12

NOTE: If gene name is provided, the chromosomal location (RefSeq) will be automatically provided and does not need to be entered UNLESS you are providing exons.

CB

Optional

Public

VUS: What is the protocol for interpreting a variation as a VUS? Describe how your lab interprets a variation as a VUS.
CC

Optional

Public

VUS: What software is used to interpret novel variations? Describe the software your lab uses to interpret novel variations. You can include lab-developed software.
CD

Optional

Public

VUS: What is the laboratory's policy on reporting novel variations? Describe how your lab reports novel variations.
CE

Optional

Public

VUS: Are family members recruited without charge?

Select from the provided options:

Not provided
Yes
No
Decline to answer

CF/td>

Optional

Public

VUS: Comments about recruiting family members. Describe if your lab offers testing for a variant of unknown significance to family members free of charge; for example, to affected individuals and/or presumed obligate carriers to help determine clinical significance of a VUS. Write an explanation or give information about who would be eligible to testing free of charge and how the lab does it.
CG

Optional

Public

VUS: Will the lab re-contact the ordering physician if variant interpretation changes?

Select from the provided options:

Not provided
Yes
No
Decline to answer

CH

Optional

Public

VUS: Comments about re-contacting the ordering physician Type a description or explanation about how the lab monitors and addresses reinterpretation of genetic test results over time, after issuing the report. For example, is there a time limit, do you systematically re-evaluate prior interpretations and generate new reports, or does the person ordering the test need to peridically recontact the laboratry to inquire about changes in test interpretation?
CI

Optional

Public

VUS: Research performed after clinical testing is complete Describe any research testing being performed using the submitted sample after clinical testing is complete. For example, research testing is allowed under IRB approved protocols or the patient would have to sign an informed consent for the research protocol. If the protocol is registered in clincaltrials.gov, you can enter that information here. Please note, Quality Control is not considered as research for this question.
CJ

Recommended

Public

Is proficiency testing performed for this test? Select Yes or No to indicate whether the test is subject to periodic internal or external evaluation of the accuracy of test results.
CK

Minimal* (if 'Yes' is selected for PT performed)

Public

Proficiency testing method

Specify which type of proficiency testing is performed. Proficiency testing is a determination of laboratory testing performance by means of interlaboratory comparisons wherby a group of laboratories receive multiple specimens for analysis and/or identification and the program compares the results among laboratories and/or with an assigned valude. Alternative assessment is the determination of laboratory testing performance by means other than PT such as split-sample testing or testing by a different method. Choices include:

Alternative Assessment
Formal PT program
Inter-Laboratory
Intra-Laboratory
Other

CL

Minimal* (if 'Other' is selected for PT method)

Public

Proficiency testing method, 'Other' value Enter the corresponding 'Other' value for proficiency testing method.
CM

Recommended

Public

Provider for proficiency testing

Specify the agency or society that administers the proficiency testing program for the test. Options include:

American College of Medical Genetics / College of American Pathologists, ACMG/CAP
American College of Physicians - Medical Laboratory Evaluation, ACP MLE
Association for Molecular Pathology, AMP
...


For the complete, current list of choices for this field, see ftp://ftp.ncbi.nlm.nih.gov/pub/GTR/standard_terms/Proficiency_testing_provider.txt".

CN

Minimal* (if 'Other' is selected for Provider for proficiency testing)

Public

Provider for proficiency testing other value Enter the corresponding 'Other' value for provider for proficiency testing.
CO

Recommended

Public

Description of proficiency testing method Explain proficiency testing (PT) method and provide PT scores and/or results, the PT reportable range, the PT interval and the number of specimens tested.
CP

Recommended

Public

Citations to support proficiency testing description Provide citations to support assay limitation statements. Provide PubMed ID when available, otherwise full citations or URLs. URLs should be entered with the appropriate prefix, i.e., http:// or https://. If multiple, separate by '|'.
CQ

Recommended

Public

Description of internal test validation method Explain how the laboratory validates the test.
CR

Recommended

Public

Citations to support internal test validation description Provide citations to support assay limitation statements. Provide PubMed ID when available, otherwise full citations or URLs. URLs should be entered with the appropriate prefix, i.e., http:// or https://. If multiple, separate by '|'.
CS

Recommended

Public

Major CAP category

If College of American Pathologists (CAP) is chosen as Provider for proficiency testing, select Major CAP category from list. Add multiple as needed by entering on a separate line. Choices include:

ABO Subgroup Typing
Alpha-1 Antitrypsin (SERPINA1) Genotyping
Anti-HCV, Rapid Methods, Waived...

For the complete, current list of choices for this field, see ftp://ftp.ncbi.nlm.nih.gov/pub/GTR/standard_terms/CAP_test_categories.txt.

CT

Recommended

Public

CAP category

If Major CAP category is selected, specify relevant sub-category. Add multiple as needed by entering on separate lines, corresponding to entry in column CQ. Choices include: 

10q (PTEN) deletion
ABO grouping
ABO grouping (includes A subtyping)...

For the complete, current list of choices for this field, see ftp://ftp.ncbi.nlm.nih.gov/pub/GTR/standard_terms/CAP_test_list.txt.

CU

Optional

Public

CAP test list

Choose the appropriate test code corresponding to the CAP category if provided. Choices include:

AAT
ABO
ABOSG
...

For the complete, current list of choices for this field, see ftp://ftp.ncbi.nlm.nih.gov/pub/GTR/standard_terms/CAP_test_codes.txt.

Novel Condition Tab

Column Status Description Hints
A

Minimal* (if providing novel condition)

Public

#Conditions/Phenotypes Enter your novel condition/phenotype name. To be sure the condition is novel, please search the GTR public web site (www.ncbi.nlm.nih.gov/gtr) for condition names. Note, your term may be an alternate term for a GTR condition name. Searching GTR will help prevent duplicate entries and ease test discovery for health care providers. If known, provide the term as the SNOMED CT preferred terminology.
B

Minimal* (if providing novel condition)

Private

Indication type

Choose the category most appropriate for your novel condition/phenotype term. Options include:

Disease
Pharmacological response
Named protein variant
Blood group
Finding
Quantitative trait

C

Optional

Public

Lab displayed condition preferred name If the term submitted in column A is the SNOMED CT preferred term, but you would like a different term displayed for your test, enter the alternate term here. This should be a single term.
D

Optional

Public

Suggest synonyms for condition Enter synonyms for the novel condition.
E

Optional

Public

Lab displayed acronym for the condition Enter your preferred acronym for the novel condition. This should be a single term.
F

Optional

Private

Suggest acronyms for condition Enter acronyms for the novel condition.
G

Optional

Private

Mode of inheritance for the condition

Select the mode of inheritance for the novel condition. Options include:

Autosomal dominant inheritance
Autosomal recessive inheritance
Autosomal unknown
Codominant
Genetic anticipation
Mitochondrial inheritance
Other
Sex-limited autosomal dominant
Somatic mutation
Sporadic
X-linked dominant inheritance
X-linked inheritance
X-linked recessive inheritance
Y-linked inheritance

H Minimal* (if 'Other' selected in column 'G') Mode of inheritance, 'Other' value If 'Other' was selected in column G, please specify the new term.
I

Optional

Private

Disease mechanism for the condition

Describe the disease mechanism for the relationship of condition to test target. Options include:

Other
Gain of function
Loss of function

J Minimal* (if 'Other' selected in column 'I') Disease mechanism, 'Other' value If 'Other' was selected in column I, please specify the new term.
K

Optional

Private

Prevalence (text description) Enter the prevalence, or the most current estimated number of cases of the disease in the population.
L

Optional

Private

Prevalence (URL) If 'Prevalence' is provided, either an URL or a citation is recommened to support the prevalence claim. URLs should be entered with the appropriate prefix, i.e., http:// or https://.
M

Optional

Private

Citations to support prevalence If 'Prevalence' is provided, either an URL or a citation is recommended to support the prevalence claim. Please enter PubMed ID if known, otherwise full citation.
N

Optional

Private

Comments to GTR staff about condition Enter information for GTR staff regarding the addition of a novel condition/phenotype name to the GTR database. Please include reasoning and if you searched for the term on the GTR public site. Citations are useful when GTR staff evaluates the novel condition.

Possible error messages

The following is a list of errors that may arise when your file is processed. These are the validation points that are checked and we encourage you to be aware of them so that you can avoid them when completing your file. When a file is uploaded with data that is not accepted or with missing data, you will receive an email listing the errors encountered in the file so you can make the appropriate edits. The possible error messages are:

  1. Cell with missing values (required fields only, for a list of required fields, please see the table 'Definitions and column values').

  2. Cell contains multiple values whereas only a single value is allowed.

  3. The number of values between certain cells is required to match. Some cells are interdependent; for example, each test target needs to be linked to at least one indication.

  4. The condition/phenotype name is not recognized by GTR. Please check the syntax or spelling of the terms you enter. You can find recognized terms by searching GTR.

  5. The MIM number is not recognized as a condition record. Please make sure that all MIM numbers correspond to a condition/phenotype record in OMIM (i.e. MIM numbers for gene records are not accepted as condition identifiers).

  6. The entry for 'Name of what is tested' does not match a gene symbol in the GTR database, which uses symbols from the HUGO Gene Nomenclature Committee (HGNC). Please review entries for misspellings and/or search GTR for recognized gene symbols.

  7. Value entered does notmatch any of the allowed values, e.g., in a controlled field list such as 'Purpose of the test'. Check the options available in the column.

  8. Test performance location(s): Either entire test in-house, or all test work location must be specified (Specimen preparation; Wet lab work; Interpretation; Generate reort).

  9. Permission error. If the current login account is not associated with the lab.

  10. AMA license agreement is required if CPT code is provided in excel file. The submitter must read and agree to the AMA license agreement prior to uploading a full test submission file with CPT codes entered. Please log into the submission site and review the AMA license agreement.

  11. Un-recognized column header or empty hearder in the excel fiel, e.g., certain column has been renamed by user.

  12. Excel fiel error, such as the file is not an excel file, or the file does not have a 'lab test' sheet, or we cannot read data from the file.

  13. Database error during validation. This is the rare case when the database connection is broken during validation. Please try uploading again.

Processing also checks for order codes that match tests already registered by your lab in GTR and if found, will generate a warning message. This is not considered to be an error. Laboratories may use the same order code for different tests, so this check is meant to alert you to the possibility of duplication or a typographical error in entering a code. This message is information for your consideration and will not halt processing of your file.

Follow these steps to upload a completed file

Step 1. Download the file gtr_test_submission_template.xlsx

Step 2. Complete the file

Step 3. Go to the GTR submission user interface and Loginwith your MyNCBI credentials

Step 4. Click on your laboratory name or the link 'Review lab submission' to go to your lab record

Image indicating where to click to review lab submission or go to a lab record

Step 5. Go to the Overview tab of your lab record

Overview tab

Step 6. Scroll to the bottom of the page (or use the End button on your keyboard)

Step 7. Upload the completed file.

bulk upload button

Step 8. Notification of submissions - you will receive a notification via email within a few minutes of uploading your file:

Step 9. The file you uploaded will display in the 'History of bulk test uploads' and is accessible to you. You can download that file if you need to address errors or edit data. You will also notice the date and time of upload. Please consider versioning your template if you need to make corrections so that you can later distinguish which version you uploaded to GTR.

history of bulk upload section

Step 10. Refresh the page.

tests from bulk upload

  • Browse your computer
  • Select the file
  • Click the 'Upload your bulk submission file' button
  • If your spreadsheet is successfully uploaded, you will receive an email entitled 'Your tests submitted to GTR in bulk via spreadsheet are ready for review'.
  • If your speadsheet is successfully uploaded but has tests with order codes that match tests you already submitted to GTR, you will receive an email entitled 'Your tests submitted to GTR in bulk via spreadsheet are ready for review' with a section where 'warnings' are discussed. 'Warnings' are a list of tests that have the same order codes as tests already in the GTR. You can review these tests in the submission user interface, in case they were submitted in error as duplicates or the order codes need to be edited. Distinct tests can have the same order code, so you are not required to make edits. This validation step is performed to help you detect possible duplications in your submissions.
  • If your spreadsheet contains errors and cannot be processed, you will receive error messages in the user interface and an email entitled 'Your tests submitted to GTR in bulk via spreadsheet contain processing errors which require your attention'. You will need to correct these errors and resubmit your spreadsheet. A list of errors and how to address them can be found above.
  • Once the spreadsheet has been successfully processed, the tests uploaded will display in your GTR submission homepage.
  • There is a status box on the table that tells you the file's processing status: 'success', 'warnings' or 'error'.
  • If successful, your tests will display on the GTR public web site within 24-48 hours.

Support Center

Last updated: 2018-08-27T21:18:27Z